This vignette demonstrates how to add linkouts to a NG-CHM. Linkouts allow for a deeper exploration of the NG-CHM data, for example by providing direct links to NCBI Databases, GeneCards, etc.
The needed packages are loaded and a basic NG-CHM is constructed from the sample data.
To add linkouts, the axis type is specified with chmAddAxisType(). For the demo data in this example, row labels correspond to genes, and are specified as HUGO gene symbols:
The column labels in the demo data are full 28-character TCGA aliquot barcodes:
hm <- chmAddAxisType(hm, 'column', 'bio.tcga.barcode.sample.vial.portion.analyte.aliquot')
Resulting NG-CHM
Here is the resulting NG-CHM:
Available Axis Label Types
In the above example, the axis type was ‘bio.gene.hugo’. The available axis types are:
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bio.gene.entrezid: NCBI Entrez Gene Identifier
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bio.gene.hugo: HUGO gene symbol
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bio.geo.acc: GEO accession id
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bio.go: Gene Ontology accession identifier
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bio.mdacc.pathwayid: PathwaysWeb pathway identifier
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bio.mirna: miRNA identifier
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bio.pathway.msigdb.name: msig DB pathway name
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bio.protein.uniprotid: Uniprot protein identifier
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bio.pubmed: PubMed identifier
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bio.tcga.barcode.sample: First 15 characters of TCGA aliquot barcode
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bio.tcga.barcode.sample.vial: First 16 characters of TCGA aliquot barcode
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bio.tcga.barcode.sample.vial.portion: First 19 characters of TCGA aliquot barcode
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bio.tcga.barcode.sample.vial.portion.analyte: First 20 characters of a TCGA aliquot barcode
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bio.tcga.barcode.sample.vial.portion.analyte.aliquot: Full 28 character TCGA aliquot barcode
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bio.transcript.ensembl: Ensembl transcript identifier
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bio.transcriptid: Entrez transcription identifier
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scholar: Google Scholar search term
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search: Generic search term